Solution structure of acidocin B, a circular bacteriocin produced by Lactobacillus acidophilus M46

Characterization of a novel circular bacteriocin from Bacillus velezensis 1-3, and its mode of action against Listeria monocytogenes

In this study, isolate Bacillus velezensis1-3 was selected out for its anti- Listeria potency, from which a novel circular bacteriocin, velezin, was purified out of the fermentate, and then characterized. Facilitated with a broad antibacterial spectrum, velezin has demonstrated decent inhibitive activity against of foodborne pathogen L. monocytogenes ATCC 19115. It exerted the antibacterial activity through damaging the membrane integrity of targeted cell and causing leakage of vital elements, including K+ ion. It was noteworthy that velezin also inhibited the biofilm formation by L. monocytogenes ATCC 19115. At the challenge of velezin, L. monocytogenes ATCC 19115 up-regulated expression of genes associated with membrane, ion transporters, stressing-related proteins as well as the genes responsible for the synthesis of small molecule. Taken together, velezin may have potential to be a candidate as natural additive used in food/feed in the future.

Engineering circular bacteriocins: structural and functional effects of α-helix exchanges and disulfide introductions in circularin A

Circular bacteriocins form a distinct group of antimicrobial peptides (AMPs) characterized by their unique head-to-tail ligated circular structure and functional properties. They belong to the ribosomally synthesized and post-translationally modified peptide (RiPP) family. The ribosomal origin of these peptides facilitates rapid diversification through mutations in the precursor genes combined with specific modification enzymes. In this study, we primarily explored the bacteriocin engineering potential of circularin A, a circular bacteriocin produced by Clostridium beijerinckii ATCC 25752. Specifically, we employed strategies involving α-helix replacements and disulfide bond introductions to investigate their effects on both biosynthesis and bioactivity of the bacteriocin. The results show the feasibility of peptide engineering to introduce certain structural properties into circularin A through carefully designed approaches. The introduction of cysteines for potential disulfide bonds resulted in a substantial reduction in bacteriocin biosynthesis and/or bioactivity, indicating the importance of maintaining dynamic flexibility of α-helices in circularin A, while reduction of the potential disulfide in one case increased the activity. The 5 α-helices of circularin A were respectively replaced by corresponding helices from another circular peptide, enterocin AS-48, and modestly active peptides were obtained in a few cases. Overall, this study provides valuable insights into the engineering potential of circular bacteriocins as antimicrobial agents, including their structural and functional restrictions and their suitability as peptide engineering scaffolds. This helps to pave the way for the development of novel antimicrobial peptides with tailored properties based on circular bacteriocins.

Perspectives in Searching Antimicrobial Peptides (AMPs) Produced by the Microbiota

Changes in the structure and function of the microbiota are associated with various human diseases. These microbial changes can be mediated by antimicrobial peptides (AMPs), small peptides produced by the host and their microbiota, which play a crucial role in host-bacteria co-evolution. Thus, by studying AMPs produced by the microbiota (microbial AMPs), we can better understand the interactions between host and bacteria in microbiome homeostasis. Additionally, microbial AMPs are a new source of compounds against pathogenic and multi-resistant bacteria. Further, the growing accessibility to metagenomic and metatranscriptomic datasets presents an opportunity to discover new microbial AMPs. This review examines the structural properties of microbiota-derived AMPs, their molecular action mechanisms, genomic organization, and strategies for their identification in any microbiome data as well as experimental testing. Overall, we provided a comprehensive overview of this important topic from the microbial perspective.

Genes encoding a novel thermostable bacteriocin in the thermophilic bacterium Aeribacillus pallidus PI8

AIM

Aeribacillus pallidus PI8 is a Gram-positive thermophilic bacterium that produces thermostable antimicrobial substances against several bacterial species, including Geobacillus kaustophilus HTA426. In the present study, we sought to identify genes of PI8 with antibacterial activity.

METHODS AND RESULTS

We isolated, cloned, and characterized a thermostable bacteriocin from A. pallidus PI8 and named it pallidocyclin. Mass spectrometric analyses of pallidocyclin revealed that it had a circular peptide structure, and its precursor was encoded by pcynA in the PI8 genome. pcynA is the second gene within the pcynBACDEF operon. Expression of the full-length pcynBACDEF operon in Bacillus subtilis produced intact pallidocyclin, whereas expression of pcynF in G. kaustophilus HTA426 conferred resistance to pallidocyclin.

CONCLUSION

Aeribacillus pallidus PI8 possesses the pcynBACDEF operon to produce pallidocyclin. pcynA encodes the pallidocyclin precursor, and pcynF acts as an antagonist of pallidocyclin.

Using metabolomics to understand stress responses in Lactic Acid Bacteria and their applications in the food industry

BACKGROUND

Lactic Acid Bacteria (LAB) are commonly used as starter cultures, probiotics, to produce lactic acid and other useful compounds, and even as natural preservatives. For use in any food product however, LAB need to survive the various stresses they encounter in the environment and during processing. Understanding these mechanisms may enable direction of LAB biochemistry with potential beneficial impact for the food industry.

AIM OF REVIEW

To give an overview of the use of LAB in the food industry and then generate a deeper biochemical understanding of LAB stress response mechanisms via metabolomics, and methods of screening for robust strains of LAB.

KEY SCIENTIFIC CONCEPTS OF REVIEW

Uses of LAB in food products were assessed and factors which contribute to survival and tolerance in LAB investigated. Changes in the metabolic profiles of LAB exposed to stress were found to be associated with carbohydrates, amino acids and fatty acid levels and these changes were proposed to be a result of the bacteria trying to maintain cellular homeostasis in response to external conditions and minimise cellular damage from reactive oxygen species. This correlates with morphological analysis which shows that LAB can undergo cell elongation and shortening, as well as thinning and thickening of cell membranes, when exposed to stress. It is proposed that these innate strategies can be utilised to minimise negative effects caused by stress through selection of intrinsically robust strains, genetic modification and/or prior exposure to sublethal stress. This work demonstrates the utility of metabolomics to the food industry.

Diversity of the bacteriocins, their classification and potential applications in combat of antibiotic resistant and clinically relevant pathogens

There is almost a century since discovery of penicillin by Alexander Fleming, a century of enthusiasm, abuse, facing development of antibiotic-resistance and clear conclusion that the modern medicine needs a new type of antimicrobials. Bacteriocins produced by Gram-positive and Gram-negative bacteria, Archaea and Eukaryotes were widely explored as potential antimicrobials with several applications in food industry. In last two decades bacteriocins showed their potential as promising alternative therapeutic for the treatment of antibiotic-resistant pathogens. Bacteriocins can be characterised as highly selective antimicrobials and therapeutics with low cytotoxicity. Most probably in order to solve the problems associated with the increasing number of antibiotic-resistant bacteria, the application of natural or bioengineered bacteriocins in addition to synergistically acting preparations of bacteriocins and conventional antibiotics, can be the next step in combat versus drug-resistant pathogens. In this overview we focussed on diversity of specific lactic acid bacteria and their bacteriocins. Moreover, some additional examples of bacteriocins from non-lactic acid, Gram-positive and Gram-negative bacteria, Archaea and eukaryotic organisms are presented and discussed. Therapeutic properties of bacteriocins, their bioengineering and combined applications, together with conventional antibiotics, were evaluated with the scope of application in human and veterinary medicine for combating (multi-)drug-resistant pathogens.

The Circular Bacteriocin enterocin NKR-5-3B has an Improved Stability Profile over Nisin

Bacteriocins are a large family of bacterial peptides that have antimicrobial activity and potential applications as clinical antibiotics or food preservatives. Circular bacteriocins are a unique class of these biomolecules distinguished by a seamless circular topology, and are widely assumed to be ultra-stable based on this constraining structural feature. However, without quantitative studies of their susceptibility to defined thermal, chemical, and enzymatic conditions, their stability characteristics remain poorly understood, limiting their translational development. Here, we produced the circular bacteriocin enterocin NKR-5-3B (Ent53B) in mg/L quantities using a heterologous Lactococcus expression system, and characterized its thermal stability by NMR, chemical stability by circular dichroism and analytical HPLC, and enzymatic stability by analytical HPLC. We demonstrate that Ent53B is ultra-stable, resistant to temperatures approaching boiling, acidic (pH 2.6) and alkaline (pH 9.0) conditions, the chaotropic agent 6M urea, and following incubation with a range of proteases (i.e., trypsin, chymotrypsin, pepsin, and papain), conditions under which most peptides and proteins degrade. Ent53B is stable across a broader range of pH conditions and proteases than nisin, the most widely used bacteriocin in food manufacturing. Antimicrobial assays showed that differences in stability correlated with differences in bactericidal activity. Overall, this study provides quantitative support for circular bacteriocins being an ultra-stable class of peptide molecules, suggesting easier handling and distribution options available to them in practical applications as antimicrobial agents.

Leader- and Terminal Residue Requirements for Circularin A Biosynthesis Probed by Systematic Mutational Analyses

Circularin A is a circular bacteriocin belonging to a subgroup of the ribosomally synthesized and post-translationally modified peptide (RiPP) superfamily. The post-translational biosynthesis of circular bacteriocins primarily consists of leader cleavage, core peptide circularization, and bacteriocin secretion. However, none of these processes have been fully elucidated due to the complex biosynthesis of such bacteriocins and the lack of homology to the functions of other known biosynthetic enzymes. In this study, we investigated the leader- and terminal residue requirements for the biosynthesis of circularin A by systematic mutational analyses, including the mutational effects of variable leader lengths, as well as site-directed substitutions of residues at positions near the leader cleavage site and the circularization site. Results show that the leader with only one Met residue, the shortest leader possible, is sufficient to produce mature circularin A; helix-forming short-sidechain hydrophobic residues are required at positions Val1 and Ala2 of the N-terminus to form active peptide derivatives, indicating the possible steric hindrance effect at these two positions; and an aromatic residue is required at the C-terminal Tyr69 position to produce a mature circular derivative. However, the requirements for residues at position Ala68 are much more relaxed relative to the positions of Val1 and Ala2, since even substitution with the largest possible residue, i.e., tryptophan, still allows the generation of an active Ala68Trp derivative. Our findings provide new perspectives for the biosynthesis of this short-leader circular bacteriocin, which enables the application of circular bacteriocin biosynthesis in rational modified peptide engineering.

Antimicrobial peptide production in response to gut microbiota imbalance

The gut microbiota presents essential functions in the immune response. The gut epithelium acts as a protective barrier and, therefore, can produce several antimicrobial peptides (AMPs) that can act against pathogenic microorganisms, including bacteria. Several factors cause a disturbance in gut microbiota, including the exacerbated and erroneous use of antibiotics. Antibiotic therapy has been closely related to bacterial resistance and is also correlated with undesired side-effects to the host, including the eradication of commensal bacteria. Consequently, this results in gut microbiota imbalance and inflammatory bowel diseases (IBD) development. In this context, AMPs in the gut epithelium play a restructuring role for gut microbiota. Some naturally occurring AMPs are selective for pathogenic bacteria, thus preserving the health microbiota. Therefore, AMPs produced by the host's epithelial cells represent effective molecules in treating gut bacterial infections. Bearing this in mind, this review focused on describing the importance of the host's AMPs in gut microbiota modulation and their role as anti-infective agents against pathogenic bacteria.

Mechanism of Action of Ribosomally Synthesized and Post-Translationally Modified Peptides

Ribosomally synthesized and post-translationally modified peptides (RiPPs) are a natural product class that has undergone significant expansion due to the rapid growth in genome sequencing data and recognition that they are made by biosynthetic pathways that share many characteristic features. Their mode of actions cover a wide range of biological processes and include binding to membranes, receptors, enzymes, lipids, RNA, and metals as well as use as cofactors and signaling molecules. This review covers the currently known modes of action (MOA) of RiPPs. In turn, the mechanisms by which these molecules interact with their natural targets provide a rich set of molecular paradigms that can be used for the design or evolution of new or improved activities given the relative ease of engineering RiPPs. In this review, coverage is limited to RiPPs originating from bacteria.

Biosynthesis and Production of Class II Bacteriocins of Food-Associated Lactic Acid Bacteria

Bacteriocins are ribosomally synthesized peptides made by bacteria that inhibit the growth of similar or closely related bacterial strains. Class II bacteriocins are a class of bacteriocins that are heat-resistant and do not undergo extensive posttranslational modification. In lactic acid bacteria (LAB), class II bacteriocins are widely distributed, and some of them have been successfully applied as food preservatives or antibiotic alternatives. Class II bacteriocins can be further divided into four subcategories. In the same subcategory, variations were observed in terms of amino acid identity, peptide length, pI, etc. The production of class II bacteriocin is controlled by a dedicated gene cluster located in the plasmid or chromosome. Besides the pre-bacteriocin encoding gene, the gene cluster generally includes various combinations of immunity, transportation, and regulatory genes. Among class II bacteriocin-producing LAB, some strains/species showed low yield. A multitude of fermentation factors including medium composition, temperature, and pH have a strong influence on bacteriocin production which is usually strain-specific. Consequently, scientists are motivated to develop high-yielding strains through the genetic engineering approach. Thus, this review aims to present and discuss the distribution, sequence characteristics, as well as biosynthesis of class II bacteriocins of LAB. Moreover, the integration of modern biotechnology and genetics with conventional fermentation technology to improve bacteriocin production will also be discussed in this review.

Transporter Protein-Guided Genome Mining for Head-to-Tail Cyclized Bacteriocins

Head-to-tail cyclized bacteriocins are ribosomally synthesized antimicrobial peptides that are defined by peptide backbone cyclization involving the N- and C- terminal amino acids. Their cyclic nature and overall three-dimensional fold confer superior stability against extreme pH and temperature conditions, and protease degradation. Most of the characterized head-to-tail cyclized bacteriocins were discovered through a traditional approach that involved the screening of bacterial isolates for antimicrobial activity and subsequent isolation and characterization of the active molecule. In this study, we performed genome mining using transporter protein sequences associated with experimentally validated head-to-tail cyclized bacteriocins as driver sequences to search for novel bacteriocins. Biosynthetic gene cluster analysis was then performed to select the high probability functional gene clusters. A total of 387 producer strains that encode putative head-to-tail cyclized bacteriocins were identified. Sequence and phylogenetic analyses revealed that this class of bacteriocins is more diverse than previously thought. Furthermore, our genome mining strategy captured hits that were not identified in precursor-based bioprospecting, showcasing the utility of this approach to expanding the repertoire of head-to-tail cyclized bacteriocins. This work sets the stage for future isolation of novel head-to-tail cyclized bacteriocins to serve as possible alternatives to traditional antibiotics and potentially help address the increasing threat posed by resistant pathogens.

PCR screening reveals abundance of bovicin-like bacteriocins among ruminal Streptococcus spp. isolated from beef and dairy cattle

AIMS

To investigate the inhibitory activity and the distribution of biosynthetic genes encoding bovicin-like bacteriocins among ruminal Streptococcus isolated from beef and dairy cattle.

METHODS AND RESULTS

Most isolates were classified as Streptococcus equinus and Streptococcus lutetiensis based on 16S rRNA sequencing. The antimicrobial activity of 150 ruminal streptococci isolated from beef and dairy cattle were tested by deferred inhibition assays and their genetic diversity was characterized by BOX-PCR. The frequency of biosynthetic genes associated with the biosynthesis of bovicin-like bacteriocins (bovicin HC5 and bovicin 255) was investigated by PCR screening. Approximately 33% of the ruminal streptococci isolated from Nellore heifers showed inhibitory activity in vitro with the majority harbouring genes for bacteriocin biosynthesis. In contrast, streptococci from Holstein cows showed limited inhibitory activity and a lower frequency of bacteriocin biosynthetic genes.

CONCLUSIONS

Streptococcus from the rumen of beef and dairy cattle exhibit remarkable differences in inhibitory activity and distribution of genes associated with the biosynthesis of prototypical bovicins (bovicin HC5 and bovicin 255).

SIGNIFICANCE AND IMPACT OF THE STUDY

Our findings demonstrate that bovicin HC5 is distributed among ruminal streptococci from different breeds of cattle. The high degree of conservation of the bovicin HC5 structural gene among strains of ruminal streptococci suggests that random genetic drift is not a dominant force in the evolution of this bacteriocin.

Singularities of Pyogenic Streptococcal Biofilms - From Formation to Health Implication

Biofilms are generally defined as communities of cells involved in a self-produced extracellular matrix adhered to a surface. In biofilms, the bacteria are less sensitive to host defense mechanisms and antimicrobial agents, due to multiple strategies, that involve modulation of gene expression, controlled metabolic rate, intercellular communication, composition, and 3D architecture of the extracellular matrix. These factors play a key role in streptococci pathogenesis, contributing to therapy failure and promoting persistent infections. The species of the pyogenic group together with Streptococcus pneumoniae are the major pathogens belonging the genus Streptococcus, and its biofilm growth has been investigated, but insights in the genetic origin of biofilm formation are limited. This review summarizes pyogenic streptococci biofilms with details on constitution, formation, and virulence factors associated with formation.

Crystal structure and site-directed mutagenesis of circular bacteriocin plantacyclin B21AG reveals cationic and aromatic residues important for antimicrobial activity

Plantacyclin B21AG is a circular bacteriocin produced by Lactiplantibacillus plantarum B21 which displays antimicrobial activity against various Gram-positive bacteria including foodborne pathogens, Listeria monocytogenes and Clostridium perfringens. It is a 58-amino acid cyclised antimicrobial peptide, with the N and C termini covalently linked together. The circular peptide backbone contributes to remarkable stability, conferring partial proteolytic resistance and structural integrity under a wide temperature and pH range. Here, we report the first crystal structure of a circular bacteriocin from a food grade Lactobacillus. The protein was crystallised using the hanging drop vapour diffusion method and the structure solved to a resolution of 1.8 Å. Sequence alignment against 18 previously characterised circular bacteriocins revealed the presence of conserved charged and aromatic residues. Alanine substitution mutagenesis validated the importance of these residues. Minimum inhibitory concentration analysis of these Ala mutants showed that Phe⁸Ala and Trp⁴⁵Ala mutants displayed a 48- and 32-fold reduction in activity, compared to wild type. The Lys¹⁹Ala mutant displayed the weakest activity, with a 128-fold reduction. These experiments demonstrate the relative importance of aromatic and cationic residues for the antimicrobial activity of plantacyclin B21AG and by extension, other circular bacteriocins sharing these evolutionarily conserved residues.

The role of disulfide bonds in a Solanum tuberosum saposin-like protein investigated using molecular dynamics

The Solanum tuberosum plant specific insert (StPSI) has a defensive role in potato plants, with the requirements of acidic pH and anionic lipids. The StPSI contains a set of three highly conserved disulfide bonds that bridge the protein’s helical domains. Removal of these bonds leads to enhanced membrane interactions. This work examined the effects of their sequential removal, both individually and in combination, using all-atom molecular dynamics to elucidate the role of disulfide linkages in maintaining overall protein tertiary structure. The tertiary structure was found to remain stable at both acidic (active) and neutral (inactive) pH despite the removal of disulfide linkages. The findings include how the dimer structure is stabilized and the impact on secondary structure on a residue-basis as a function of disulfide bond removal. The StPSI possesses an extensive network of inter-monomer hydrophobic interactions and intra-monomer hydrogen bonds, which is likely the key to the stability of the StPSI by stabilizing local secondary structure and the tertiary saposin-fold, leading to a robust association between monomers, regardless of the disulfide bond state. Removal of disulfide bonds did not significantly impact secondary structure, nor lead to quaternary structural changes. Instead, disulfide bond removal induces regions of amino acids with relatively higher or lower variation in secondary structure, relative to when all the disulfide bonds are intact. Although disulfide bonds are not required to preserve overall secondary structure, they may have an important role in maintaining a less plastic structure within plant cells in order to regulate membrane affinity or targeting.

Discovery and characterisation of circular bacteriocin plantacyclin B21AG from Lactiplantibacillus plantarum B21

Lactiplantibacillus plantarum B21 isolated from Vietnamese sausage (nem chua) has previously displayed broad antimicrobial activity against Gram-positive bacteria including foodborne pathogens Listeria monocytogenes and Clostridium perfringens. This study successfully identified the antimicrobial agent as plantacyclin B21AG, a 5668 Da circular bacteriocin demonstrating high thermostability, resistance to a wide range of pH, proteolytic resistance and temporal stability. We report a reverse genetics approach to identify and characterise plantacyclin B21AG from first principles. The bacteriocin was purified from culture supernatant by a three-step process consisting of concentration, n-butanol extraction and cation exchange chromatography. A de novo peptide sequencing using LC-MS/MS techniques identified two putative peptide fragments which were mapped to the genome sequence of L. plantarum B21. This revealed an ORF corresponding to a putative circular bacteriocin with a 33-amino acid leader peptide and a 58-amino acid mature peptide encoded on a native plasmid pB21AG01. The bacteriocin is shown to be a small cationic predominantly α-helical protein (69%). The corresponding gene cluster, consisted of seven genes associated with post-translational circularisation, immunity and secretion. Whilst plantacyclin B21AG is 86% identical to the newly published plantaricyclin A it is more highly cationic having a net charge of +3 due to an additional basic residue in the putative membrane interaction region. This and other substitutions may well go some way to explaining functional differences. The robust nature of plantacyclin B21AG, its antimicrobial activity and associated machinery for cyclisation make it an interesting biotechnological target for development, both as a food-safe antimicrobial or potentially a platform technology for recombinant protein circularisation.

In Silico Analysis Highlights the Diversity and Novelty of Circular Bacteriocins in Sequenced Microbial Genomes

Consumer demand for “fresh food” with no chemical preservatives has prompted researchers to pay more attention to natural antimicrobial peptides such as bacteriocins. Nisin is currently the most widely used food biopreservative among the bacteriocins; however, its applications are restricted due to its low stability at neutral and alkaline pH values. Circular bacteriocins have potent antimicrobial activity against foodborne pathogens, show exceptional stability, and have great potential to be developed as biopreservatives. Here, we take advantage of the precursor peptides of 15 reported circular bacteriocins to devise an in silico approach to identify potential circular bacteriocins in sequenced microbial genomes. A total of nearly 7,000 putative precursor peptides were identified from 86 species of bacteria and further classified into 28 groups based on their amino acid similarity. Among the groups, 19 showed low similarity (less than 50%) to any known precursor peptide of circular bacteriocins. One novel circular bacteriocin in group 11, cerecyclin, showed the highest identity (34%) to the known circular bacteriocin enterocin NKR-5-3B and was selected for verification. Cerecyclin showed antimicrobial activity against several Gram-positive bacteria, inhibited the outgrowth of Bacillus cereus spores, and did not exhibit hemolysis activity. Moreover, it showed 4-fold- to 8-fold-higher antimicrobial activity against B. cereus and Listeria monocytogenes than nisin A. Cerecyclin also had increased stability compared to nisin A under neutral or alkaline conditions. This work not only identified a promising food biopreservative but also provided a rich source for novel circular bacteriocins.

IMPORTANCE Circular bacteriocins are promising biopreservatives, and it is important to identify more novel circular bacteriocins to enhance the current arsenal of antimicrobials. In this study, we used an in silico approach to identify a large number of novel circular bacteriocins and classified these bacteriocins into 28 groups rather than the 2 groups that were described in previous studies. Nineteen groups were novel and had low similarity (less than 50%) to any known precursor peptides of circular bacteriocins; this finding greatly expands the awareness of the novelty and diversity of circular bacteriocins. A novel circular bacteriocin which we named cerecyclin was identified in the B. cereus group; this circular bacteriocin had great antimicrobial activity against some foodborne pathogens and showed extreme stability. This study not only identified a promising food biopreservative but also provided a rich source for the identification of novel circular bacteriocins and the development of new biopreservatives.

Bioinformatic prospecting and phylogenetic analysis reveals 94 undescribed circular bacteriocins and key motifs

Background

Circular bacteriocins are antimicrobial peptides produced by bacteria with a N and C termini ligation. They have desirable properties such as activity at low concentrations along with thermal, pH and proteolytic resistance. There are twenty experimentally confirmed circular bacteriocins as part of bacteriocin gene clusters, with transport, membrane and immunity proteins. Traditionally, novel antimicrobials are found by testing large numbers of isolates against indicator strains, with no promise of corresponding novel sequence.

Results

Through bioprospecting publicly available sequence databases, we identified ninety-nine circular bacteriocins across a variety of bacteria bringing the total to 119. They were grouped into two families within class I modified bacteriocins (i and ii) and further divided into subfamilies based on similarity to experimentally confirmed circular bacteriocins. Within subfamilies, sequences overwhelmingly shared similar characteristics such as sequence length, presence of a polybasic region, conserved locations of aromatic residues, C and N termini, gene clusters similarity, translational coupling and hydrophobicity profiles. At least ninety were predicted to be putatively functional based on gene clusters. Furthermore, bacteriocins identified from Enterococcus, Staphylococcus and Streptococcus species may have activity against clinically relevant strains, due to the presence of putative immunity genes required for expression in a toxin-antitoxin system. Some strains such as Paenibacillus larvae subsp. pulvifaciens SAG 10367 contained multiple circular bacteriocin gene clusters from different subfamilies, while some strains such as Bacillus cereus BCE-01 contained clusters with multiple circular bacteriocin structural genes.

Conclusions

Sequence analysis provided rapid insight into identification of novel, putative circular bacteriocins, as well as conserved genes likely essential for circularisation. This represents an expanded library of putative antimicrobial proteins which are potentially active against human, plant and animal pathogens.

Antagonistic effects of Streptococcus and Lactobacillus probiotics in pharyngeal biofilms

Direct antagonism towards pathogens including Streptococcus pyogenes is a proposed mechanism of pharyngeal probiosis but off-target effects on the symbiotic microbiota of the throat are possible and may be beneficial, harmful or neutral. We have assessed the bacteriological effects of two candidate Lactobacillus probiotics and the established pharyngeal probiotic Streptococcus salivarius K12. Antagonism towards S. pyogenes and potential off-target effects were determined using sessile monospecies biofilms and pharyngeal microcosms, respectively. The candidate probiotics were antagonistic towards S. pyogenes (rank order of increasing potency, Lactobacillus acidophilus < Lactobacillus plantarum < Streptococcus salivarius) in the absence of significant acidification or cell-cell contact. Streptococcus salivarius and L. plantarum caused significant reductions in viable counts of streptococci in pharyngeal microbiotas, whilst S. salivarius also caused reductions in staphylococci. In contrast, changes in pharyngeal eubacterial DNA profiles were limited overall. In summary, the three candidate probiotics suppressed axenic Streptococcus pyogenes biofilms by mechanisms that did not depend on cell-cell contact or acidification and did not markedly destabilize complex pharyngeal microbiotas derived from healthy individuals. SIGNIFICANCE AND IMPACT OF THE STUDY: Candidate probiotic bacteria deployed to prevent or treat bacterial pharyngitis will interact with the target bacteria such as Streptococcus pyogenes as well as with the microbiota of the throat, where off-target effects are possible. Three candidate probiotics Lactobacillus acidophilus, Lactobacillus plantarum and Streptococcus salivarius reduced viability within extant S. pyogenes biofilms through the elaboration of diffusible factors other than fermentation acids but did not markedly disrupt ex situ pharyngeal microcosms. This work demonstrates the application of in vitro pharyngeal models in the preclinical testing of the safety and efficacy of candidate pharyngeal probiotics.

The expanding structural variety among bacteriocins from Gram-positive bacteria

Bacteria use various strategies to compete in an ecological niche, including the production of bacteriocins. Bacteriocins are ribosomally synthesized antibacterial peptides, and it has been postulated that the majority of Gram-positive bacteria produce one or more of these natural products. Bacteriocins can be used in food preservation and are also considered as potential alternatives to antibiotics. The majority of bacteriocins from Gram-positive bacteria had been traditionally divided into two major classes, namely lantibiotics, which are post-translationally modified bacteriocins, and unmodified bacteriocins. The last decade has seen an expanding number of ribosomally synthesized and post-translationally modified peptides (RiPPs) in Gram-positive bacteria that have antibacterial activity. These include linear azol(in)e-containing peptides, thiopeptides, bottromycins, glycocins, lasso peptides and lipolanthines. In addition, the three-dimensional (3D) structures of a number of modified and unmodified bacteriocins have been elucidated in recent years. This review gives an overview on the structural variety of bacteriocins from Gram-positive bacteria. It will focus on the chemical and 3D structures of these peptides, and their interactions with receptors and membranes, structure-function relationships and possible modes of action.

Preservation of Meat Products with Bacteriocins Produced by Lactic Acid Bacteria Isolated from Meat

Bacteriocins are ribosomal-synthesized antimicrobial peptides that inhibit the growing of pathogenic and/or deteriorating bacteria. The most studied bacteriocin-producing microorganisms are lactic acid bacteria (LAB), as they have great potential application in food biopreservation, since the majority have GRAS (Generally Recognized as Safe) status. The LAB-producing bacteriocins and/or bacteriocins produced by these bacteria have been widely studied, with the emphasis on those derived from milk and dairy products. On the other hand, isolates from meat and meat products are less studied. The objective of this review is to address the main characteristics, classification, and mechanism of action of bacteriocins and their use in food, to highlight studies on the isolation of LAB with bacteriocinogenic potential from meat and meat products and also to characterize, purify, and apply these bacteriocins in meat products. In summary, most of the microorganisms studied areLactococcus,Enterococcus,Pediococcus, andLactobacillus, which produce bacteriocins such as nisin, enterocin, pediocin, pentocin, and sakacin, many with the potential for use in food biopreservation.

Bacteria Hunt Bacteria through an Intriguing Cyclic Peptide

In the last few decades, peptides have been victorious over small molecules as therapeutics due to their broad range of applications, high biological activity, and high specificity. However, the main challenges to overcome if peptides are to become effective drugs is their low oral bioavailability and instability under physiological conditions. Cyclic peptides play a vital role in this context because they show higher stability under physiological conditions, higher membrane permeability, and greater oral bioavailability than that of their corresponding linear analogues. In this regard, cyclic antimicrobial peptides (AMPs) have gained considerable attention in the field of novel antibiotic development. Bacterial strains produce cyclic AMPs through two pathways: ribosomal and nonribosomal. This review provides an overview of the chemical classification of cyclic AMPs isolated from bacteria, and provides a description of their biological activity and mode of action.

Circular and Leaderless Bacteriocins: Biosynthesis, Mode of Action, Applications, and Prospects

Bacteriocins are a huge family of ribosomally synthesized peptides known to exhibit a range of bioactivities, most predominantly antibacterial activities. Bacteriocins from lactic acid bacteria are of particular interest due to the latter's association to food fermentation and the general notion of them to be safe. Among the family of bacteriocins, the groups known as circular bacteriocins and leaderless bacteriocins are gaining more attention due to their enormous potential for industrial application. Circular bacteriocins and leaderless bacteriocins, arguably the least understood groups of bacteriocins, possess distinctively peculiar characteristics in their structures and biosynthetic mechanisms. Circular bacteriocins have N-to-C- terminal covalent linkage forming a structurally distinct circular peptide backbone. The circular nature of their structures provides them superior stability against various stresses compared to most linear bacteriocins. The molecular mechanism of their biosynthesis, albeit has remained poorly understood, is believed to possesses huge application prospect as it can serve as scaffold in bioengineering other biologically important peptides. On the other hand, while most bacteriocins are synthesized as inactive precursor peptides, which possess an N-terminal leader peptide attached to a C-terminal propeptide, leaderless bacteriocins are atypical as they do not have an N-terminal leader peptide, hence the name. Leaderless bacteriocins are active right after translation as they do not undergo any post-translational processing common to other groups of bacteriocins. This "simplicity" in the biosynthesis of leaderless bacteriocins offers a huge commercial potential as scale-up production systems are considerably easier to assemble. In this review, we summarize the current studies of both circular and leaderless bacteriocins, highlighting the progress in understanding their biosynthesis, mode of action, application and their prospects.

Bioinspired Designs, Molecular Premise and Tools for Evaluating the Ecological Importance of Antimicrobial Peptides

This review article provides an overview of recent developments in antimicrobial peptides (AMPs), summarizing structural diversity, potential new applications, activity targets and microbial killing responses in general. The use of artificial and natural AMPs as templates for rational design of peptidomimetics are also discussed and some strategies are put forward to curtail cytotoxic effects against eukaryotic cells. Considering the heat-resistant nature, chemical and proteolytic stability of AMPs, we attempt to summarize their molecular targets, examine how these macromolecules may contribute to potential environmental risks vis-à-vis the activities of the peptides. We further point out the evolutional characteristics of the macromolecules and indicate how they can be useful in designing target-specific peptides. Methods are suggested that may help to assess toxic mechanisms of AMPs and possible solutions are discussed to promote the development and application of AMPs in medicine. Even if there is wide exposure to the environment like in the hospital settings, AMPs may instead contribute to prevent healthcare-associated infections so long as ecotoxicological aspects are considered.

Metabolomics of Early Stage Plant Cell-Microbe Interaction Using Stable Isotope Labeling

Metabolomics has been used in unraveling metabolites that play essential roles in plant-microbe (including pathogen) interactions. However, the problem of profiling a plant metabolome with potential contaminating metabolites from the coexisting microbes has been largely ignored. To address this problem, we implemented an effective stable isotope labeling approach, where the metabolome of a plant bacterial pathogen Pseudomonas syringae pv. tomato (Pst) DC3000 was labeled with heavy isotopes. The labeled bacterial cells were incubated with Arabidopsis thaliana epidermal peels (EPs) with guard cells, and excessive bacterial cells were subsequently removed from the plant tissues by washing. The plant metabolites were characterized by liquid chromatography mass spectrometry using multiple reactions monitoring, which can differentiate plant and bacterial metabolites. Targeted metabolomic analysis suggested that Pst DC3000 infection may modulate stomatal movement by reprograming plant signaling and primary metabolic pathways. This proof-of-concept study demonstrates the utility of this strategy in differentiation of the plant and microbe metabolomes, and it has broad applications in studying metabolic interactions between microbes and other organisms.

Plantaricyclin A, a Novel Circular Bacteriocin Produced by Lactobacillus plantarum NI326: Purification, Characterization, and Heterologous Production

Bacteriocins from lactic acid bacteria (LAB) are of increasing interest in recent years due to their potential as natural preservatives against food and beverage spoilage microorganisms. In a screening study for LAB, we isolated from olives a strain, Lactobacillus plantarum NI326, with activity against the beverage-spoilage bacterium Alicyclobacillus acidoterrestris Genome sequencing of NI326 enabled the identification of a gene cluster (designated plc) encoding a putative circular bacteriocin and proteins involved in its modification, transport, and immunity. This novel bacteriocin, named plantaricyclin A (PlcA), was grouped into the circular bacteriocin subgroup II due to its high degree of similarity with other gassericin A-like bacteriocins. Purification of PlcA from the supernatant of Lb. plantarum NI326 resulted in an active peptide with a molecular mass of 5,570 Da, corresponding to that predicted from the (processed) PlcA amino acid sequence. The plc gene cluster was cloned and expressed in Lactococcus lactis NZ9000, resulting in the production of an active 5,570-Da bacteriocin in the supernatant. PlcA is believed to be produced as a 91-amino-acid precursor with a 33-amino-acid leader peptide, which is predicted to be removed, followed by joining of the N and C termini via a covalent linkage to form the mature 58-amino-acid circular bacteriocin PlcA. We report the characterization of a circular bacteriocin produced by Lb. plantarum The inhibition displayed against A. acidoterrestris highlights its potential use as a preservative in food and beverages.IMPORTANCE In this work, we describe the purification and characterization of an antimicrobial peptide, termed plantaricyclin A (PlcA), produced by a Lactobacillus plantarum strain isolated from olives. This peptide has a circular structure, and all genes involved in its production, circularization, and secretion were identified. PlcA shows antimicrobial activity against different strains, including Alicyclobacillus acidoterrestris, a common spoilage bacterium, which causes substantial economic losses in the beverage industry every year. In this study, we describe a circular antimicrobial peptide, PlcA, for a Lactobacillus plantarum strain.

Strategies for Pathogen Biocontrol Using Lactic Acid Bacteria and Their Metabolites: A Focus on Meat Ecosystems and Industrial Environments

The globalization of trade and lifestyle ensure that the factors responsible for the emergence of diseases are more present than ever. Despite biotechnology advancements, meat-based foods are still under scrutiny because of the presence of pathogens, which causes a loss of consumer confidence and consequently a fall in demand. In this context, Lactic Acid Bacteria (LAB) as GRAS organisms offer an alternative for developing pathogen-free foods, particularly avoiding Listeria monocytogenes, with minimal processing and fewer additives while maintaining the foods' sensorial characteristics. The use of LAB strains, enabling us to produce antimicrobial peptides (bacteriocins) in addition to lactic acid, with an impact on quality and safety during fermentation, processing, and/or storage of meat and ready-to-eat (RTE) meat products, constitutes a promising tool. A number of bacteriocin-based strategies including the use of bioprotective cultures, purified and/or semi-purified bacteriocins as well as their inclusion in varied packaging materials under different storage conditions, have been investigated. The application of bacteriocins as part of hurdle technology using non-thermal technologies was explored for the preservation of RTE meat products. Likewise, considering that food contamination with L. monocytogenes is a consequence of the post-processing manipulation of RTE foods, the role of bacteriocinogenic LAB in the control of biofilms formed on industrial surfaces is also discussed.

Bacteriocin Gene-Trait matching across the complete Lactobacillus Pan-genome

Lactobacilli constitute a large genus of Gram-positive lactic acid bacteria which have widespread roles ranging from gut commensals to starters in fermented foods. A combination of in silico and laboratory-based screening allowed us to determine the overall bacteriocin producing potential of representative strains of each species of the genus. The genomes of 175 lactobacilli and 38 associated species were screened for the presence of antimicrobial producing genes and combined with screening for antimicrobial activity against a range of indicators. There also appears to be a link between the strains' environment and bacteriocin production, with those from the animal and human microbiota encoding over twice as many bacteriocins as those from other sources. Five novel bacteriocins were identified belonging to differing bacteriocin classes, including two-peptide bacteriocins (muricidin and acidocin X) and circular bacteriocins (paracyclicin). In addition, there was a clear clustering of helveticin type bacteriolysins in the Lactobacillus acidophilus group of species. This combined in silico and in vitro approach to screening has demonstrated the true diversity and complexity of bacteriocins across the genus. It also highlights their biological importance in terms of communication and competition between closely related strains in diverse complex microbial environments.

Structural features of many circular and leaderless bacteriocins are similar to those in saposins and saposin-like peptides

Bacteriocins are potent antimicrobial peptides that are ribosomally produced and exported by bacteria, presumably to aid elimination of competing microorganisms. Many circular and linear leaderless bacteriocins have a recuring three dimensional structural motif known as a saposin-like fold. Although these bacteriocin sizes and sequences are often quite different, and their mechanisms of action vary, this conserved motif of multiple helices appears critical for activity and may enable peptide-lipid and peptide-receptor interactions in target bacterial cell membranes. Comparisons between electrostatic surfaces and hydrophobic surface maps of different bacteriocins are discussed emphasizing similarities and differences in the context of proposed modes of action.

Bacteriocins from lactic acid bacteria and their applications in meat and meat products

Meat and meat products have always been an important part of human diet, and contain valuable nutrients for growth and health. Nevertheless, they are perishable and susceptible to microbial contamination, leading to an increased health risk for consumers as well as to the economic loss in meat industry. The utilization of bacteriocins produced by lactic acid bacteria (LAB) as a natural preservative has received a considerable attention. Inoculation of bacteriocin-producing LAB cell as starter or protective cultures is suitable for fermented meats, whilst the direct addition of bacteriocin as food additive is more preferable when live cells of LAB could not produce bacteriocin in the real meat system. The incorporation of bacteriocins in packaging is another way to improve meat safety to avoid direct addition of bacteriocin to meat. Utilization of bacteriocins can effectively contribute to food safety, especially when integrated into hurdle concepts. In this review, LAB bacteriocins and their applications in meat and meat products are revisited. The molecular structure and characteristics of bacteriocins recently discovered, as well as exemplary properties are also discussed.

Bacteriocins of lactic acid bacteria: extending the family

Lactic acid bacteria (LAB) constitute a heterogeneous group of microorganisms that produce lactic acid as the major product during the fermentation process. LAB are Gram-positive bacteria with great biotechnological potential in the food industry. They can produce bacteriocins, which are proteinaceous antimicrobial molecules with a diverse genetic origin, posttranslationally modified or not, that can help the producer organism to outcompete other bacterial species. In this review, we focus on the various types of bacteriocins that can be found in LAB and the organization and regulation of the gene clusters responsible for their production and biosynthesis, and consider the food applications of the prototype bacteriocins from LAB. Furthermore, we propose a revised classification of bacteriocins that can accommodate the increasing number of classes reported over the last years.

Functional Analysis of Genes Involved in the Biosynthesis of Enterocin NKR-5-3B, a Novel Circular Bacteriocin

A putative biosynthetic gene cluster of the enterocin NKR-5-3B (Ent53B), a novel circular bacteriocin, was analyzed by sequencing the flanking regions around enkB, the Ent53B structural gene, using a fosmid library. A region approximately 9 kb in length was obtained, and the enkB1, enkB2, enkB3, and enkB4 genes, encoding putative biosynthetic proteins involved in the production, maturation, and secretion of Ent53B, were identified. We also determined the identity of proteins mediating self-immunity against the effects of Ent53B. Heterologous expression systems in various heterologous hosts, such as Enterococcus faecalis and Lactococcus lactis strains, were successfully established. The production and secretion of the mature Ent53B required the cooperative functions of five genes. Ent53B was produced only by those heterologous hosts that expressed protein products of the enkB, enkB1, enkB2, enkB3, and enkB4 genes. Moreover, self-immunity against the antimicrobial action of Ent53B was conferred by at least two independent mechanisms. Heterologous hosts harboring the intact enkB4 gene and/or a combination of intact enkB1 and enkB3 genes were immune to the inhibitory action of Ent53B.

IMPORTANCE

In addition to their potential application as food preservatives, circular bacteriocins are now considered possible alternatives to therapeutic antibiotics due to the exceptional stability conferred by their circular structure. The successful practical application of circular bacteriocins will become possible only if the molecular details of their biosynthesis are fully understood. The results of the present study offer a new perspective on the possible mechanism of circular bacteriocin biosynthesis. In addition, since some enterococcal strains are associated with pathogenicity, virulence, and drug resistance, the establishment of the first multigenus host heterologous production of Ent53B has very high practical significance, as it widens the scope of possible Ent53B applications.

Nuclear Magnetic Resonance Solution Structures of Lacticin Q and Aureocin A53 Reveal a Structural Motif Conserved among Leaderless Bacteriocins with Broad-Spectrum Activity

Lacticin Q (LnqQ) and aureocin A53 (AucA) are leaderless bacteriocins from Lactococcus lactis QU5 and Staphylococcus aureus A53, respectively. These bacteriocins are characterized by the absence of an N-terminal leader sequence and are active against a broad range of Gram-positive bacteria. LnqQ and AucA consist of 53 and 51 amino acids, respectively, and have 47% identical sequences. In this study, their three-dimensional structures were elucidated using solution nuclear magnetic resonance and were shown to consist of four α-helices that assume a very similar compact, globular overall fold (root-mean-square deviation of 1.7 Å) with a highly cationic surface and a hydrophobic core. The structures of LnqQ and AucA resemble the shorter two-component leaderless bacteriocins, enterocins 7A and 7B, despite having low levels of sequence identity. Homology modeling revealed that the observed structural motif may be shared among leaderless bacteriocins with broad-spectrum activity against Gram-positive organisms. The elucidated structures of LnqQ and AucA also exhibit some resemblance to circular bacteriocins. Despite their similar overall fold, inhibition studies showed that LnqQ and AucA have different antimicrobial potency against the Gram-positive strains tested, suggesting that sequence disparities play a crucial role in their mechanisms of action.

Solution Structure of Enterocin HF, an Antilisterial Bacteriocin Produced by Enterococcus faecium M3K31

The solution structure of enterocin HF (EntHF), a class IIa bacteriocin of 43 amino acids produced by Enterococcus faecium M3K31, was evaluated by CD and NMR spectroscopy. Purified EntHF was unstructured in water, but CD analysis supports that EntHF adopts an α-helical conformation when exposed to increasing concentrations of trifluoroethanol. Furthermore, NMR spectroscopy indicates that this bacteriocin adopts an antiparallel β-sheet structure in the N-terminal region (residues 1-17), followed by a well-defined central α-helix (residues 19-30) and a more disordered C-terminal end (residues 31-43). EntHF could be structurally organized into three flexible regions that might act in a coordinated manner. This is in agreement with the absence of long-range nuclear Overhauser effect signals between the β-sheet domain and the C-terminal end of the bacteriocin. The 3D structure recorded for EntHF fits emerging facts regarding target recognition and mode of action of class IIa bacteriocins.